Nadal is the No.3 seed at the All England Club, with Federer second despite being below his old foe in the world rankings.
Federer's superior achievements on grass over the previous two years are the reason for the Swiss great being the No.2 seed rather than Nadal.
Nadal stated "it's not only about grass", but Federer says rules should be respected.
"There's not much we the players can add to the story, other than we just deal with it," the eight-time Wimbledon champion said.
"At the end of the day, if you want to win the tournament, you got to go through all the players that are in front of you. And now that the draw is out, we move on.
"But we knew that the system was in place. I guess the system rewards you for playing a lot on the grass, well on grass."
Federer will take on South African outsider Lloyd Harris in the first round and could face Nadal in the semi-finals, although the 12-time French Open champion may have to beat the likes of Nick Kyrgios, Marin Cilic and Dominic Thiem to reach the last four.